fix(mcp): ensure proper environment variable override semantics

Use a map to merge environment variables with guaranteed override
behavior. Config variables (cfg.Env) now properly override file
variables (envFile), which in turn override parent process environment.

Previously, simply appending to a slice could result in duplicate
variables, and while most systems use the last occurrence, this
behavior is not guaranteed and could lead to unexpected results.

Addresses Copilot code review feedback.

pkg/mcp/manager.go

@@ -284,8 +284,16 @@ func (m *Manager) ConnectServer(ctx context.Context, name string, cfg config.MCP
 		// Create command with context
 		cmd := exec.CommandContext(ctx, cfg.Command, cfg.Args...)
 
-		// Set environment variables
-		env := cmd.Environ()
+		// Build environment variables with proper override semantics
+		// Use a map to ensure config variables override file variables
+		envMap := make(map[string]string)
+
+		// Start with parent process environment
+		for _, e := range cmd.Environ() {
+			if idx := strings.Index(e, "="); idx > 0 {
+				envMap[e[:idx]] = e[idx+1:]
+			}
+		}
 
 		// Load environment variables from file if specified
 		if cfg.EnvFile != "" {
@@ -294,7 +302,7 @@ func (m *Manager) ConnectServer(ctx context.Context, name string, cfg config.MCP
 				return fmt.Errorf("failed to load env file %s: %w", cfg.EnvFile, err)
 			}
 			for k, v := range envVars {
-				env = append(env, fmt.Sprintf("%s=%s", k, v))
+				envMap[k] = v
 			}
 			logger.DebugCF("mcp", "Loaded environment variables from file",
 				map[string]interface{}{
@@ -305,16 +313,16 @@ func (m *Manager) ConnectServer(ctx context.Context, name string, cfg config.MCP
 		}
 
 		// Environment variables from config override those from file
-		if len(cfg.Env) > 0 {
-			for k, v := range cfg.Env {
-				env = append(env, fmt.Sprintf("%s=%s", k, v))
-			}
+		for k, v := range cfg.Env {
+			envMap[k] = v
 		}
 
-		// Set environment if we added any variables
-		if len(env) > len(cmd.Environ()) {
-			cmd.Env = env
+		// Convert map to slice
+		env := make([]string, 0, len(envMap))
+		for k, v := range envMap {
+			env = append(env, fmt.Sprintf("%s=%s", k, v))
 		}
+		cmd.Env = env
 
 		transport = &mcp.CommandTransport{Command: cmd}
 	default: